Integration of David Corsars Phylip File support

[jalview.git] / src / jalview / io / FileParse.java

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 62237d9..e8e9f2e 100755 (executable)
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -1,24 +1,28 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
 import java.io.*;
 import java.net.*;
+import java.util.zip.GZIPInputStream;
 
 /**
  * implements a random access wrapper around a particular datasource, for
@@ -46,7 +50,7 @@ public class FileParse
 
   public void setNewlineString(String nl)
   {
-    newline = nl;
+      newline = nl;
   }
 
   public String getNewlineString()
@@ -141,18 +145,73 @@ public class FileParse
     }
     if (!error)
     {
+      if (fileStr.toLowerCase().endsWith(".gz"))
+      {
+        try
+        {
+          dataIn = tryAsGzipSource(new FileInputStream(fileStr));
+          dataName = fileStr;
+          return error;
+        } catch (Exception x)
+        {
+          warningMessage = "Failed  to resolve as a GZ stream ("
+                  + x.getMessage() + ")";
+          x.printStackTrace();
+        }
+        ;
+      }
+
       dataIn = new BufferedReader(new FileReader(fileStr));
       dataName = fileStr;
     }
     return error;
   }
 
+  private BufferedReader tryAsGzipSource(InputStream inputStream)
+          throws Exception
+  {
+    BufferedReader inData = new BufferedReader(new InputStreamReader(
+            new GZIPInputStream(inputStream)));
+    inData.mark(2048);
+    inData.read();
+    inData.reset();
+    return inData;
+  }
+
   private boolean checkURLSource(String fileStr) throws IOException,
           MalformedURLException
   {
     errormessage = "URL NOT FOUND";
     URL url = new URL(fileStr);
-    dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
+    //
+    // GZIPInputStream code borrowed from Aquaria (soon to be open sourced) via
+    // Kenny Sabir
+    Exception e = null;
+    if (fileStr.toLowerCase().endsWith(".gz"))
+    {
+      try
+      {
+        InputStream inputStream = url.openStream();
+        dataIn = tryAsGzipSource(inputStream);
+        dataName = fileStr;
+        return false;
+      } catch (Exception ex)
+      {
+        e = ex;
+      }
+    }
+
+    try
+    {
+      dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
+    } catch (IOException q)
+    {
+      if (e != null)
+      {
+        throw new IOException("Failed to resolve GZIP stream", e);
+      }
+      throw q;
+    }
     // record URL as name of datasource.
     dataName = fileStr;
     return false;